Publication: Small Ancestry Informative Marker panels for complete classification between the original four HapMap populations
Issued Date
2012-11-27
Resource Type
ISSN
17485681
17485673
17485673
Other identifier(s)
2-s2.0-84869751554
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Mahidol University
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SCOPUS
Bibliographic Citation
International Journal of Data Mining and Bioinformatics. Vol.6, No.6 (2012), 651-674
Suggested Citation
Damrongrit Setsirichok, Theera Piroonratana, Anunchai Assawamakin, Touchpong Usavanarong, Chanin Limwongse, Waranyu Wongseree, Chatchawit Aporntewan, Nachol Chaiyaratana Small Ancestry Informative Marker panels for complete classification between the original four HapMap populations. International Journal of Data Mining and Bioinformatics. Vol.6, No.6 (2012), 651-674. doi:10.1504/IJDMB.2012.050249 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/13571
Research Projects
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Title
Small Ancestry Informative Marker panels for complete classification between the original four HapMap populations
Abstract
A protocol for the identification of Ancestry Informative Markers (AIMs) from genome-wide Single Nucleotide Polymorphism (SNP) data is proposed. The protocol consists of three main steps: identification of potential positive selection regions via F ST extremity measurement, SNP screening via two-stage attribute selection and classification model construction using a Naïve Bayes classifier. The two-stage attribute selection is composed of a newly developed round robin Symmetrical Uncertainty (SU) ranking technique and a wrapper embedded with a Naïve Bayes classifier. The protocol has been applied to the HapMap Phase II data. Two AIM panels, which consist of 10 and 16 SNPs that lead to complete classification between CEU, CHB, JPT and YRI populations, are identified. Moreover, the panels are at least four times smaller than those reported in previous studies. The results suggest that the protocol could be useful in a scenario involving a larger number of populations. Copyright © 2012 Inderscience Enterprises Ltd.